Multiple sequence alignment - TraesCS5A01G519600

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5A01G519600 chr5A 100.000 5531 0 0 1 5531 680920288 680925818 0.000000e+00 10214
1 TraesCS5A01G519600 chr5A 88.261 3646 401 13 904 4535 680981087 680984719 0.000000e+00 4337
2 TraesCS5A01G519600 chr4B 94.331 4551 237 7 1 4539 643527187 643531728 0.000000e+00 6955
3 TraesCS5A01G519600 chr4B 92.281 3679 254 18 872 4539 643481745 643485404 0.000000e+00 5193
4 TraesCS5A01G519600 chr4B 88.442 3634 393 12 915 4535 643629028 643632647 0.000000e+00 4359
5 TraesCS5A01G519600 chrUn 93.963 4572 206 22 1 4539 60418201 60413667 0.000000e+00 6850
6 TraesCS5A01G519600 chrUn 94.522 4235 185 21 339 4539 16761860 16757639 0.000000e+00 6492
7 TraesCS5A01G519600 chrUn 92.907 2580 174 8 1965 4539 60473879 60471304 0.000000e+00 3742
8 TraesCS5A01G519600 chrUn 82.977 981 140 15 4552 5523 119056884 119057846 0.000000e+00 861
9 TraesCS5A01G519600 chr4D 91.328 3667 291 16 881 4539 500197094 500200741 0.000000e+00 4985
10 TraesCS5A01G519600 chr4D 88.269 3640 401 11 908 4535 500300861 500304486 0.000000e+00 4333
11 TraesCS5A01G519600 chr7D 82.569 981 157 12 4561 5531 580762239 580761263 0.000000e+00 852
12 TraesCS5A01G519600 chr2B 81.323 862 137 11 4552 5398 10990197 10991049 0.000000e+00 678
13 TraesCS5A01G519600 chr2B 81.445 609 102 8 4923 5523 717823122 717822517 6.440000e-134 488
14 TraesCS5A01G519600 chr1A 80.449 890 158 12 4552 5432 569445399 569444517 0.000000e+00 665
15 TraesCS5A01G519600 chr1A 79.821 223 41 4 4680 4898 20805120 20804898 5.730000e-35 159
16 TraesCS5A01G519600 chr4A 80.613 815 146 9 4552 5358 624635049 624635859 2.190000e-173 619
17 TraesCS5A01G519600 chr7B 75.877 456 88 17 4636 5081 540712005 540712448 4.340000e-51 213
18 TraesCS5A01G519600 chr7B 80.741 135 25 1 4562 4696 145819669 145819536 2.730000e-18 104
19 TraesCS5A01G519600 chr6A 79.672 305 53 8 4628 4930 40230826 40230529 1.560000e-50 211
20 TraesCS5A01G519600 chr6B 75.799 438 92 10 4636 5070 159134155 159134581 5.610000e-50 209


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G519600 chr5A 680920288 680925818 5530 False 10214 10214 100.000 1 5531 1 chr5A.!!$F1 5530
1 TraesCS5A01G519600 chr5A 680981087 680984719 3632 False 4337 4337 88.261 904 4535 1 chr5A.!!$F2 3631
2 TraesCS5A01G519600 chr4B 643527187 643531728 4541 False 6955 6955 94.331 1 4539 1 chr4B.!!$F2 4538
3 TraesCS5A01G519600 chr4B 643481745 643485404 3659 False 5193 5193 92.281 872 4539 1 chr4B.!!$F1 3667
4 TraesCS5A01G519600 chr4B 643629028 643632647 3619 False 4359 4359 88.442 915 4535 1 chr4B.!!$F3 3620
5 TraesCS5A01G519600 chrUn 60413667 60418201 4534 True 6850 6850 93.963 1 4539 1 chrUn.!!$R2 4538
6 TraesCS5A01G519600 chrUn 16757639 16761860 4221 True 6492 6492 94.522 339 4539 1 chrUn.!!$R1 4200
7 TraesCS5A01G519600 chrUn 60471304 60473879 2575 True 3742 3742 92.907 1965 4539 1 chrUn.!!$R3 2574
8 TraesCS5A01G519600 chrUn 119056884 119057846 962 False 861 861 82.977 4552 5523 1 chrUn.!!$F1 971
9 TraesCS5A01G519600 chr4D 500197094 500200741 3647 False 4985 4985 91.328 881 4539 1 chr4D.!!$F1 3658
10 TraesCS5A01G519600 chr4D 500300861 500304486 3625 False 4333 4333 88.269 908 4535 1 chr4D.!!$F2 3627
11 TraesCS5A01G519600 chr7D 580761263 580762239 976 True 852 852 82.569 4561 5531 1 chr7D.!!$R1 970
12 TraesCS5A01G519600 chr2B 10990197 10991049 852 False 678 678 81.323 4552 5398 1 chr2B.!!$F1 846
13 TraesCS5A01G519600 chr2B 717822517 717823122 605 True 488 488 81.445 4923 5523 1 chr2B.!!$R1 600
14 TraesCS5A01G519600 chr1A 569444517 569445399 882 True 665 665 80.449 4552 5432 1 chr1A.!!$R2 880
15 TraesCS5A01G519600 chr4A 624635049 624635859 810 False 619 619 80.613 4552 5358 1 chr4A.!!$F1 806

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
857 891 0.036577 CCTCAGCTTCCACTCCACAG 60.037 60.000 0.00 0.00 0.00 3.66 F
1346 1446 0.740737 AACAATAGCTTCCATGGCGC 59.259 50.000 6.96 12.32 34.52 6.53 F
1641 1741 1.268992 TGCTTACCGGCACCATACCT 61.269 55.000 0.00 0.00 37.29 3.08 F
1676 1776 1.797046 CAGTCGCCATCTCACATATGC 59.203 52.381 1.58 0.00 0.00 3.14 F
2175 2275 2.089868 TGGCTACACCCTCCCCAATATA 60.090 50.000 0.00 0.00 37.83 0.86 F
3422 3522 2.417239 CCCATTTGCAACATGACAATGC 59.583 45.455 17.70 5.17 37.29 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2518 2618 0.690192 TTGAGGTTGCCAATCTCCGA 59.310 50.000 14.91 1.27 0.00 4.55 R
2744 2844 2.221169 TGGTGAGTTGAGTGCATTGTC 58.779 47.619 0.00 0.00 0.00 3.18 R
3605 3705 0.396060 GAAGCTCCTATCTGCCCCAG 59.604 60.000 0.00 0.00 0.00 4.45 R
3804 3904 6.071320 AGTCCTTTGGCTTAAACTCAGAATT 58.929 36.000 0.00 0.00 0.00 2.17 R
4237 4342 0.685097 TCAGTTGGACTACACCCTGC 59.315 55.000 0.00 0.00 31.52 4.85 R
4895 5002 0.254178 ATCTGAACTCGCCATGCCTT 59.746 50.000 0.00 0.00 0.00 4.35 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 4.344359 TGGCAGTGTGTATGTGAACTTA 57.656 40.909 0.00 0.00 0.00 2.24
73 74 4.905429 TGGCAGTGTGTATGTGAACTTAT 58.095 39.130 0.00 0.00 0.00 1.73
74 75 5.312895 TGGCAGTGTGTATGTGAACTTATT 58.687 37.500 0.00 0.00 0.00 1.40
75 76 5.767665 TGGCAGTGTGTATGTGAACTTATTT 59.232 36.000 0.00 0.00 0.00 1.40
76 77 6.072728 TGGCAGTGTGTATGTGAACTTATTTC 60.073 38.462 0.00 0.00 34.41 2.17
77 78 6.149474 GGCAGTGTGTATGTGAACTTATTTCT 59.851 38.462 0.00 0.00 34.97 2.52
78 79 7.308589 GGCAGTGTGTATGTGAACTTATTTCTT 60.309 37.037 0.00 0.00 34.97 2.52
137 138 6.603237 TGACTGCTTGATTTTATATGACGG 57.397 37.500 0.00 0.00 0.00 4.79
139 140 5.437060 ACTGCTTGATTTTATATGACGGGT 58.563 37.500 0.00 0.00 0.00 5.28
149 150 0.042131 TATGACGGGTCTGGGGTTCT 59.958 55.000 0.00 0.00 0.00 3.01
150 151 0.840722 ATGACGGGTCTGGGGTTCTT 60.841 55.000 0.00 0.00 0.00 2.52
163 164 2.541556 GGGTTCTTGACGATGACTAGC 58.458 52.381 0.00 0.00 0.00 3.42
179 180 4.118410 GACTAGCACTGACAATCATCCAG 58.882 47.826 0.00 0.00 0.00 3.86
190 191 6.425735 TGACAATCATCCAGTGTAATCCAAT 58.574 36.000 0.00 0.00 31.97 3.16
232 233 6.942576 ACAACTTGCTAAGAACTCCATATTGT 59.057 34.615 3.37 0.00 0.00 2.71
266 267 2.193536 GCCAACAACCGCTTCCAGT 61.194 57.895 0.00 0.00 0.00 4.00
309 310 5.589855 CAGGCAGATATGTAATCCAAACACA 59.410 40.000 0.00 0.00 0.00 3.72
454 458 4.414846 AGCATTTGTTCTATCCAGGATCCT 59.585 41.667 9.02 9.02 0.00 3.24
480 484 1.699634 AGGAAGCTAAGCTCACAACCA 59.300 47.619 0.00 0.00 38.25 3.67
519 523 2.557056 GGTACCTTTGAAACCTTGCTCC 59.443 50.000 4.06 0.00 0.00 4.70
526 530 0.402121 GAAACCTTGCTCCCTCCAGT 59.598 55.000 0.00 0.00 0.00 4.00
730 756 0.662619 CATGCGTCACTTGGTTGTGT 59.337 50.000 0.00 0.00 38.90 3.72
778 812 2.540515 CTCTGGTATTGTGTACCTGCG 58.459 52.381 5.89 0.00 38.39 5.18
803 837 1.007734 CCAGCATGATCGCATTGCC 60.008 57.895 2.41 0.00 39.69 4.52
842 876 4.703897 CAAACCACACTTAGAAGTCCTCA 58.296 43.478 0.00 0.00 37.08 3.86
843 877 4.608948 AACCACACTTAGAAGTCCTCAG 57.391 45.455 0.00 0.00 37.08 3.35
844 878 2.300437 ACCACACTTAGAAGTCCTCAGC 59.700 50.000 0.00 0.00 37.08 4.26
845 879 2.564947 CCACACTTAGAAGTCCTCAGCT 59.435 50.000 0.00 0.00 37.08 4.24
846 880 3.007398 CCACACTTAGAAGTCCTCAGCTT 59.993 47.826 0.00 0.00 37.08 3.74
847 881 4.241681 CACACTTAGAAGTCCTCAGCTTC 58.758 47.826 0.00 0.00 41.78 3.86
848 882 3.259625 ACACTTAGAAGTCCTCAGCTTCC 59.740 47.826 0.00 0.00 42.27 3.46
849 883 3.259374 CACTTAGAAGTCCTCAGCTTCCA 59.741 47.826 0.00 0.00 42.27 3.53
850 884 3.259625 ACTTAGAAGTCCTCAGCTTCCAC 59.740 47.826 0.00 0.00 42.27 4.02
851 885 2.022718 AGAAGTCCTCAGCTTCCACT 57.977 50.000 0.00 0.00 42.27 4.00
852 886 1.899142 AGAAGTCCTCAGCTTCCACTC 59.101 52.381 0.00 0.00 42.27 3.51
853 887 0.980423 AAGTCCTCAGCTTCCACTCC 59.020 55.000 0.00 0.00 0.00 3.85
854 888 0.178921 AGTCCTCAGCTTCCACTCCA 60.179 55.000 0.00 0.00 0.00 3.86
855 889 0.036858 GTCCTCAGCTTCCACTCCAC 60.037 60.000 0.00 0.00 0.00 4.02
856 890 0.471780 TCCTCAGCTTCCACTCCACA 60.472 55.000 0.00 0.00 0.00 4.17
857 891 0.036577 CCTCAGCTTCCACTCCACAG 60.037 60.000 0.00 0.00 0.00 3.66
858 892 0.972134 CTCAGCTTCCACTCCACAGA 59.028 55.000 0.00 0.00 0.00 3.41
859 893 1.554160 CTCAGCTTCCACTCCACAGAT 59.446 52.381 0.00 0.00 0.00 2.90
860 894 2.762887 CTCAGCTTCCACTCCACAGATA 59.237 50.000 0.00 0.00 0.00 1.98
1026 1126 2.466846 ACTTTGTTGTTTCCAGGCCTT 58.533 42.857 0.00 0.00 0.00 4.35
1093 1193 5.106791 CCATCATTAGGAATCTGCGATGAAC 60.107 44.000 0.00 0.00 31.56 3.18
1169 1269 3.563390 GCTGGATTTCTAGCTTCATGGAC 59.437 47.826 8.50 0.00 45.52 4.02
1213 1313 3.499737 GGCACGGAATCACCTGCG 61.500 66.667 0.00 0.00 40.82 5.18
1245 1345 2.486504 CGGCATGTCATTGCGCTT 59.513 55.556 9.73 0.00 43.71 4.68
1346 1446 0.740737 AACAATAGCTTCCATGGCGC 59.259 50.000 6.96 12.32 34.52 6.53
1371 1471 2.607750 TCCGAGCTTGGCCTCCTT 60.608 61.111 16.01 0.00 0.00 3.36
1432 1532 4.028993 GAAGGTAACATCCCACCTGAAA 57.971 45.455 0.00 0.00 44.55 2.69
1464 1564 3.677963 CCAGCTCCAAATTCTGGGT 57.322 52.632 2.80 0.00 46.44 4.51
1497 1597 2.196925 CCTCCGTGGAGAGATCCCG 61.197 68.421 17.52 0.00 44.53 5.14
1512 1612 1.302033 CCCGCATAGCCTTAGCCAG 60.302 63.158 0.00 0.00 41.25 4.85
1611 1711 1.699656 CGCTGCGCATGCTAGTTCTT 61.700 55.000 23.05 0.00 43.34 2.52
1641 1741 1.268992 TGCTTACCGGCACCATACCT 61.269 55.000 0.00 0.00 37.29 3.08
1676 1776 1.797046 CAGTCGCCATCTCACATATGC 59.203 52.381 1.58 0.00 0.00 3.14
2066 2166 2.851263 ACGAACAACTTATCTGGGCA 57.149 45.000 0.00 0.00 0.00 5.36
2079 2179 4.717313 GGGCAGGTTCCACCGTCC 62.717 72.222 0.00 0.00 44.90 4.79
2175 2275 2.089868 TGGCTACACCCTCCCCAATATA 60.090 50.000 0.00 0.00 37.83 0.86
2221 2321 3.770933 CAGTTTTGATGGACCAATCCCAT 59.229 43.478 0.00 0.00 45.59 4.00
2284 2384 8.258708 ACCTGAACACTAATAGATTTACTGGAC 58.741 37.037 0.00 0.00 0.00 4.02
2385 2485 6.045955 GGGCTTTGTCTCTTCACTATCTAAG 58.954 44.000 0.00 0.00 0.00 2.18
2518 2618 7.363793 GCAACAAAATTTCTGGACCTATACCAT 60.364 37.037 0.00 0.00 36.79 3.55
2744 2844 5.992217 GTGGAAGAATACCTGCAAGTATAGG 59.008 44.000 8.38 0.00 40.01 2.57
3235 3335 7.993101 AGGAAATGATCATCTGTGTACAATTG 58.007 34.615 9.06 3.24 0.00 2.32
3422 3522 2.417239 CCCATTTGCAACATGACAATGC 59.583 45.455 17.70 5.17 37.29 3.56
3605 3705 9.132521 CATCAAGATTTTTGACCTTGACATTAC 57.867 33.333 0.00 0.00 45.92 1.89
3804 3904 6.546484 AGATCCTGAAGATGGTGAAAAGAAA 58.454 36.000 0.00 0.00 34.42 2.52
4082 4184 8.502387 GGTGAGATAAGCTTATTTGCAAGATAG 58.498 37.037 19.77 0.00 34.99 2.08
4118 4222 8.786826 TGTTCCTTATGGAGTTGTACAAATAG 57.213 34.615 10.51 2.85 44.24 1.73
4237 4342 5.578727 GGAGTGCTTCTGTTACAACTGATAG 59.421 44.000 2.99 5.25 36.86 2.08
4403 4508 3.907894 TTGCGTCATCCCACTTTTAAC 57.092 42.857 0.00 0.00 0.00 2.01
4507 4612 2.046988 TGGCCTCAGACACATGCG 60.047 61.111 3.32 0.00 0.00 4.73
4529 4634 5.390885 GCGTGTCTGATGAAGCAAAGAATTA 60.391 40.000 0.00 0.00 0.00 1.40
4535 4640 3.855689 TGAAGCAAAGAATTAGCAGGC 57.144 42.857 0.00 0.00 0.00 4.85
4539 4644 2.948315 AGCAAAGAATTAGCAGGCTAGC 59.052 45.455 6.04 6.04 0.00 3.42
4540 4645 2.033927 GCAAAGAATTAGCAGGCTAGCC 59.966 50.000 27.19 27.19 34.23 3.93
4541 4646 2.246719 AAGAATTAGCAGGCTAGCCG 57.753 50.000 27.83 22.20 41.95 5.52
4542 4647 1.414158 AGAATTAGCAGGCTAGCCGA 58.586 50.000 27.83 12.07 41.95 5.54
4543 4648 1.069358 AGAATTAGCAGGCTAGCCGAC 59.931 52.381 27.83 22.65 41.95 4.79
4544 4649 0.106894 AATTAGCAGGCTAGCCGACC 59.893 55.000 27.83 18.93 41.95 4.79
4545 4650 1.048724 ATTAGCAGGCTAGCCGACCA 61.049 55.000 27.83 10.54 41.95 4.02
4546 4651 1.956629 TTAGCAGGCTAGCCGACCAC 61.957 60.000 27.83 15.93 41.95 4.16
4547 4652 4.840005 GCAGGCTAGCCGACCACC 62.840 72.222 27.83 9.95 41.95 4.61
4548 4653 4.162690 CAGGCTAGCCGACCACCC 62.163 72.222 27.83 1.35 41.95 4.61
4549 4654 4.715130 AGGCTAGCCGACCACCCA 62.715 66.667 27.83 0.00 41.95 4.51
4550 4655 3.480133 GGCTAGCCGACCACCCAT 61.480 66.667 20.16 0.00 0.00 4.00
4556 4661 2.954684 GCCGACCACCCATGTGAGA 61.955 63.158 0.00 0.00 45.76 3.27
4570 4675 5.360591 CCATGTGAGATAACCCTCTTACAC 58.639 45.833 1.43 0.00 42.41 2.90
4591 4697 0.608640 GCCGATCCCAGGATAATCGT 59.391 55.000 14.20 0.00 40.41 3.73
4616 4722 1.380524 GCAGACCGCTAGAGACTACA 58.619 55.000 0.00 0.00 37.77 2.74
4617 4723 1.332375 GCAGACCGCTAGAGACTACAG 59.668 57.143 0.00 0.00 37.77 2.74
4626 4732 3.181498 GCTAGAGACTACAGGACCGAAAC 60.181 52.174 0.00 0.00 0.00 2.78
4657 4763 1.194781 AGACCTGAGAACACCGCCAT 61.195 55.000 0.00 0.00 0.00 4.40
4668 4774 1.002624 ACCGCCATACAACACCCTG 60.003 57.895 0.00 0.00 0.00 4.45
4685 4791 1.561542 CCTGGAACACCTAAGCTCCAT 59.438 52.381 0.00 0.00 37.34 3.41
4698 4804 1.811266 CTCCATGACAACGCCCTCG 60.811 63.158 0.00 0.00 42.43 4.63
4755 4862 2.938838 TCCAACGGACAAGGTTTTCAT 58.061 42.857 0.00 0.00 0.00 2.57
4757 4864 2.621055 CCAACGGACAAGGTTTTCATCA 59.379 45.455 0.00 0.00 0.00 3.07
4790 4897 1.142748 GAGAGGAGCACCATGACGG 59.857 63.158 2.07 0.00 42.50 4.79
4800 4907 0.250124 ACCATGACGGCGTCTTCAAA 60.250 50.000 36.17 19.46 39.03 2.69
4805 4912 2.281517 TGACGGCGTCTTCAAAAAGAA 58.718 42.857 36.17 13.02 43.04 2.52
4834 4941 4.736631 CGAGCGTCGCAGTCGTCA 62.737 66.667 21.09 0.00 41.79 4.35
4878 4985 2.464403 GGTAGCTCCCCCATGCCAT 61.464 63.158 0.00 0.00 0.00 4.40
4895 5002 3.009363 TGCCATCATGAGGTCTTCAAGAA 59.991 43.478 6.62 0.00 37.11 2.52
4900 5008 3.072915 TCATGAGGTCTTCAAGAAAGGCA 59.927 43.478 0.00 0.00 41.63 4.75
4909 5017 0.883833 CAAGAAAGGCATGGCGAGTT 59.116 50.000 14.30 9.48 0.00 3.01
4919 5027 0.692419 ATGGCGAGTTCAGATCCCCT 60.692 55.000 0.00 0.00 0.00 4.79
4926 5034 0.620556 GTTCAGATCCCCTGCTCCAA 59.379 55.000 0.00 0.00 42.62 3.53
4930 5038 0.849417 AGATCCCCTGCTCCAAATCC 59.151 55.000 0.00 0.00 0.00 3.01
4934 5048 2.677228 CCTGCTCCAAATCCGGGT 59.323 61.111 0.00 0.00 0.00 5.28
4965 5079 1.595093 CGAAGACAAATGGCCCACCC 61.595 60.000 0.00 0.00 33.59 4.61
4977 5091 3.330720 CCACCCGAGCCTTTCCCT 61.331 66.667 0.00 0.00 0.00 4.20
4999 5113 0.594602 TACACCTCTTGTCGTCCACG 59.405 55.000 0.00 0.00 39.91 4.94
5011 5125 4.373116 TCCACGCGACCAAGAGGC 62.373 66.667 15.93 0.00 39.06 4.70
5033 5147 4.343323 CCACCACCACCGCCATGA 62.343 66.667 0.00 0.00 0.00 3.07
5035 5149 2.114670 CACCACCACCGCCATGATC 61.115 63.158 0.00 0.00 0.00 2.92
5095 5209 2.670934 CGCCCTGACTTGCAAGCT 60.671 61.111 26.27 13.39 0.00 3.74
5096 5210 2.960170 GCCCTGACTTGCAAGCTG 59.040 61.111 26.27 19.84 0.00 4.24
5097 5211 1.601759 GCCCTGACTTGCAAGCTGA 60.602 57.895 26.27 9.26 0.00 4.26
5105 5220 1.415659 ACTTGCAAGCTGAGAGACACT 59.584 47.619 26.27 0.00 0.00 3.55
5111 5226 2.499289 CAAGCTGAGAGACACTACCCAT 59.501 50.000 0.00 0.00 0.00 4.00
5112 5227 2.106566 AGCTGAGAGACACTACCCATG 58.893 52.381 0.00 0.00 0.00 3.66
5122 5237 0.759346 ACTACCCATGATCCGCTTCC 59.241 55.000 0.00 0.00 0.00 3.46
5149 5264 1.229428 CAAACTGCGGCAAGAGAAGA 58.771 50.000 3.44 0.00 0.00 2.87
5151 5266 0.946221 AACTGCGGCAAGAGAAGACG 60.946 55.000 3.44 0.00 0.00 4.18
5153 5268 2.261671 GCGGCAAGAGAAGACGGA 59.738 61.111 0.00 0.00 0.00 4.69
5184 5303 4.101448 GGGTCAGCGCCACCATCT 62.101 66.667 23.78 0.00 35.35 2.90
5248 5377 0.107945 GGGACATGACTCAGTGGCTC 60.108 60.000 0.00 0.00 0.00 4.70
5253 5382 1.064906 CATGACTCAGTGGCTCCCAAT 60.065 52.381 0.00 0.00 34.18 3.16
5276 5405 2.558359 GCCATTGTTGAGTAACCAGCTT 59.442 45.455 0.00 0.00 35.92 3.74
5278 5407 4.399303 GCCATTGTTGAGTAACCAGCTTAT 59.601 41.667 0.00 0.00 35.92 1.73
5286 5415 2.424601 AGTAACCAGCTTATACGACGCA 59.575 45.455 0.00 0.00 0.00 5.24
5319 5448 4.778143 GGCACCGATCCAACCGCT 62.778 66.667 0.00 0.00 0.00 5.52
5350 5479 1.993391 CCCCGACCACCACTACCAT 60.993 63.158 0.00 0.00 0.00 3.55
5358 5487 1.573108 CACCACTACCATGGACCTCT 58.427 55.000 21.47 0.00 43.02 3.69
5361 5490 2.315155 ACCACTACCATGGACCTCTACT 59.685 50.000 21.47 0.00 43.02 2.57
5440 5569 1.764854 AGAGGTGTCCCAACCACGT 60.765 57.895 0.00 0.00 43.20 4.49
5442 5571 2.191109 GGTGTCCCAACCACGTGT 59.809 61.111 15.65 0.00 40.22 4.49
5453 5582 0.036388 ACCACGTGTAGGGAGCAATG 60.036 55.000 15.65 0.00 0.00 2.82
5459 5588 2.093973 CGTGTAGGGAGCAATGAACTCT 60.094 50.000 0.00 0.00 34.46 3.24
5472 5601 0.907230 GAACTCTGGGCAGGAGGACT 60.907 60.000 9.98 0.00 35.34 3.85
5488 5617 1.623811 GGACTAGGTCAAACTCCTGCA 59.376 52.381 0.00 0.00 36.60 4.41
5491 5620 0.320374 TAGGTCAAACTCCTGCACGG 59.680 55.000 0.00 0.00 36.60 4.94
5492 5621 1.070786 GGTCAAACTCCTGCACGGA 59.929 57.895 5.03 5.03 40.30 4.69
5493 5622 1.228657 GGTCAAACTCCTGCACGGAC 61.229 60.000 1.25 0.00 36.69 4.79
5495 5624 1.594293 CAAACTCCTGCACGGACGT 60.594 57.895 0.00 0.00 36.69 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 8.165239 TGTCTTGCATAGTCAACTACAAAAAT 57.835 30.769 0.00 0.00 0.00 1.82
137 138 0.613777 ATCGTCAAGAACCCCAGACC 59.386 55.000 0.00 0.00 0.00 3.85
139 140 1.275291 GTCATCGTCAAGAACCCCAGA 59.725 52.381 0.00 0.00 0.00 3.86
149 150 2.556622 TGTCAGTGCTAGTCATCGTCAA 59.443 45.455 0.00 0.00 0.00 3.18
150 151 2.159382 TGTCAGTGCTAGTCATCGTCA 58.841 47.619 0.00 0.00 0.00 4.35
179 180 4.941263 TGTCAGGTTGCTATTGGATTACAC 59.059 41.667 0.00 0.00 0.00 2.90
190 191 0.753867 TGTCCGTTGTCAGGTTGCTA 59.246 50.000 0.00 0.00 0.00 3.49
232 233 0.901114 TGGCGCTCCACTTGTACCTA 60.901 55.000 7.64 0.00 37.47 3.08
266 267 1.299648 CTGGCGACCCTTGGATCAA 59.700 57.895 0.00 0.00 0.00 2.57
296 297 5.475564 ACAATGGTAGGTGTGTTTGGATTAC 59.524 40.000 0.00 0.00 0.00 1.89
299 300 3.826157 CACAATGGTAGGTGTGTTTGGAT 59.174 43.478 0.00 0.00 40.22 3.41
309 310 1.614317 GCTTCCAGCACAATGGTAGGT 60.614 52.381 2.22 0.00 41.89 3.08
321 322 1.135575 GCTAACACACATGCTTCCAGC 60.136 52.381 0.00 0.00 42.82 4.85
454 458 1.985159 TGAGCTTAGCTTCCTTTGGGA 59.015 47.619 8.58 0.00 39.88 4.37
480 484 5.070685 GGTACCAGGAGTCAAAATGAGTTT 58.929 41.667 7.15 0.00 28.50 2.66
539 543 8.892723 CAAATGCACTAGTTGATTAATGAGGTA 58.107 33.333 0.00 0.00 36.50 3.08
690 714 7.278646 CGCATGACAAGCCAGTATATATACAAT 59.721 37.037 22.00 2.67 35.74 2.71
693 717 6.100004 ACGCATGACAAGCCAGTATATATAC 58.900 40.000 14.05 14.05 0.00 1.47
694 718 6.071616 TGACGCATGACAAGCCAGTATATATA 60.072 38.462 0.00 0.00 0.00 0.86
695 719 5.152623 ACGCATGACAAGCCAGTATATAT 57.847 39.130 0.00 0.00 0.00 0.86
730 756 1.296392 CTGATGACGTTGGCAGGGA 59.704 57.895 0.00 0.00 0.00 4.20
842 876 1.484240 GCTATCTGTGGAGTGGAAGCT 59.516 52.381 0.00 0.00 0.00 3.74
843 877 1.474143 GGCTATCTGTGGAGTGGAAGC 60.474 57.143 0.00 0.00 0.00 3.86
844 878 2.102252 GAGGCTATCTGTGGAGTGGAAG 59.898 54.545 0.00 0.00 0.00 3.46
845 879 2.111384 GAGGCTATCTGTGGAGTGGAA 58.889 52.381 0.00 0.00 0.00 3.53
846 880 1.689575 GGAGGCTATCTGTGGAGTGGA 60.690 57.143 0.00 0.00 0.00 4.02
847 881 0.755686 GGAGGCTATCTGTGGAGTGG 59.244 60.000 0.00 0.00 0.00 4.00
848 882 1.137872 GTGGAGGCTATCTGTGGAGTG 59.862 57.143 0.00 0.00 0.00 3.51
849 883 1.273267 TGTGGAGGCTATCTGTGGAGT 60.273 52.381 0.00 0.00 0.00 3.85
850 884 1.489481 TGTGGAGGCTATCTGTGGAG 58.511 55.000 0.00 0.00 0.00 3.86
851 885 2.180946 ATGTGGAGGCTATCTGTGGA 57.819 50.000 0.00 0.00 0.00 4.02
852 886 4.564406 GGAATATGTGGAGGCTATCTGTGG 60.564 50.000 0.00 0.00 0.00 4.17
853 887 4.285517 AGGAATATGTGGAGGCTATCTGTG 59.714 45.833 0.00 0.00 0.00 3.66
854 888 4.497516 AGGAATATGTGGAGGCTATCTGT 58.502 43.478 0.00 0.00 0.00 3.41
855 889 5.486526 GAAGGAATATGTGGAGGCTATCTG 58.513 45.833 0.00 0.00 0.00 2.90
856 890 4.534103 GGAAGGAATATGTGGAGGCTATCT 59.466 45.833 0.00 0.00 0.00 1.98
857 891 4.534103 AGGAAGGAATATGTGGAGGCTATC 59.466 45.833 0.00 0.00 0.00 2.08
858 892 4.507342 AGGAAGGAATATGTGGAGGCTAT 58.493 43.478 0.00 0.00 0.00 2.97
859 893 3.904339 GAGGAAGGAATATGTGGAGGCTA 59.096 47.826 0.00 0.00 0.00 3.93
860 894 2.708325 GAGGAAGGAATATGTGGAGGCT 59.292 50.000 0.00 0.00 0.00 4.58
1026 1126 2.930826 AGAGGCAGAGAAACCGAAAA 57.069 45.000 0.00 0.00 0.00 2.29
1146 1246 2.883386 CCATGAAGCTAGAAATCCAGCC 59.117 50.000 0.00 0.00 38.61 4.85
1169 1269 1.219522 GAACTCCGTGGACGTGTTGG 61.220 60.000 0.00 0.00 35.48 3.77
1181 1281 2.811317 GCCAGTCGCAGAACTCCG 60.811 66.667 0.00 0.00 39.69 4.63
1346 1446 3.114616 CAAGCTCGGACGGCACAG 61.115 66.667 0.00 0.00 0.00 3.66
1371 1471 0.541063 TGAGGTTGGTGAGTCGGCTA 60.541 55.000 0.00 0.00 0.00 3.93
1432 1532 0.917533 AGCTGGGAACATGCAGAGAT 59.082 50.000 0.00 0.00 41.51 2.75
1497 1597 0.464373 TGCACTGGCTAAGGCTATGC 60.464 55.000 12.05 12.05 41.91 3.14
1512 1612 1.208614 CTCTTGAAGGCGCTTGCAC 59.791 57.895 7.64 0.00 41.71 4.57
1602 1702 3.429881 GCATGTTTTTGGCAAGAACTAGC 59.570 43.478 27.29 25.21 0.00 3.42
1611 1711 1.000283 CCGGTAAGCATGTTTTTGGCA 60.000 47.619 0.00 0.00 0.00 4.92
1641 1741 2.032528 CTGCTGCCCAAAGACGGA 59.967 61.111 0.00 0.00 0.00 4.69
1676 1776 1.242076 GGCATTCATCCCAAGATCGG 58.758 55.000 0.00 0.00 0.00 4.18
2079 2179 6.766429 TCTCAGGGATGACATATTGAAGATG 58.234 40.000 0.00 0.00 0.00 2.90
2175 2275 9.303116 CTGTTATATGAGAGTATTAGGTCCTGT 57.697 37.037 0.00 0.00 0.00 4.00
2221 2321 4.081420 GTGGTATGCTTTGAGAAGAGAGGA 60.081 45.833 0.00 0.00 34.71 3.71
2284 2384 3.459232 TGAGCCGAAGAATGGTATGAG 57.541 47.619 0.00 0.00 0.00 2.90
2385 2485 2.175878 ACATGTTCAGTCTGGAGCAC 57.824 50.000 0.00 0.00 30.63 4.40
2518 2618 0.690192 TTGAGGTTGCCAATCTCCGA 59.310 50.000 14.91 1.27 0.00 4.55
2744 2844 2.221169 TGGTGAGTTGAGTGCATTGTC 58.779 47.619 0.00 0.00 0.00 3.18
3235 3335 2.554893 GAGACATACCTCTCATCGGGAC 59.445 54.545 0.00 0.00 37.27 4.46
3422 3522 3.132629 TCTCTAGCTTCTTTACGTGCG 57.867 47.619 0.00 0.00 0.00 5.34
3605 3705 0.396060 GAAGCTCCTATCTGCCCCAG 59.604 60.000 0.00 0.00 0.00 4.45
3804 3904 6.071320 AGTCCTTTGGCTTAAACTCAGAATT 58.929 36.000 0.00 0.00 0.00 2.17
4082 4184 4.825085 TCCATAAGGAACAAACAGAACCAC 59.175 41.667 0.00 0.00 42.23 4.16
4237 4342 0.685097 TCAGTTGGACTACACCCTGC 59.315 55.000 0.00 0.00 31.52 4.85
4403 4508 1.487976 TGGAGCAAGAGAGGCCTATTG 59.512 52.381 4.42 12.90 42.75 1.90
4507 4612 6.026513 GCTAATTCTTTGCTTCATCAGACAC 58.973 40.000 0.00 0.00 0.00 3.67
4529 4634 3.775654 GTGGTCGGCTAGCCTGCT 61.776 66.667 30.55 0.00 0.00 4.24
4535 4640 1.153369 CACATGGGTGGTCGGCTAG 60.153 63.158 0.00 0.00 41.45 3.42
4539 4644 1.119684 TATCTCACATGGGTGGTCGG 58.880 55.000 0.00 0.00 45.32 4.79
4540 4645 2.550978 GTTATCTCACATGGGTGGTCG 58.449 52.381 0.00 0.00 45.32 4.79
4541 4646 2.421529 GGGTTATCTCACATGGGTGGTC 60.422 54.545 0.00 0.00 45.32 4.02
4542 4647 1.564348 GGGTTATCTCACATGGGTGGT 59.436 52.381 0.00 0.00 45.32 4.16
4543 4648 1.846439 AGGGTTATCTCACATGGGTGG 59.154 52.381 0.00 0.00 45.32 4.61
4544 4649 2.774234 AGAGGGTTATCTCACATGGGTG 59.226 50.000 0.00 0.00 46.66 4.61
4545 4650 3.136641 AGAGGGTTATCTCACATGGGT 57.863 47.619 0.00 0.00 36.30 4.51
4546 4651 4.408921 TGTAAGAGGGTTATCTCACATGGG 59.591 45.833 0.00 0.00 36.30 4.00
4547 4652 5.104941 TGTGTAAGAGGGTTATCTCACATGG 60.105 44.000 0.00 0.00 32.26 3.66
4548 4653 5.977635 TGTGTAAGAGGGTTATCTCACATG 58.022 41.667 0.00 0.00 32.26 3.21
4549 4654 5.395768 GCTGTGTAAGAGGGTTATCTCACAT 60.396 44.000 0.00 0.00 35.03 3.21
4550 4655 4.081642 GCTGTGTAAGAGGGTTATCTCACA 60.082 45.833 0.00 0.00 34.61 3.58
4556 4661 2.463752 TCGGCTGTGTAAGAGGGTTAT 58.536 47.619 0.00 0.00 0.00 1.89
4570 4675 1.404717 CGATTATCCTGGGATCGGCTG 60.405 57.143 5.29 0.00 39.07 4.85
4616 4722 2.635915 TCCTGTGTTATGTTTCGGTCCT 59.364 45.455 0.00 0.00 0.00 3.85
4617 4723 3.048337 TCCTGTGTTATGTTTCGGTCC 57.952 47.619 0.00 0.00 0.00 4.46
4657 4763 1.513858 AGGTGTTCCAGGGTGTTGTA 58.486 50.000 0.00 0.00 35.89 2.41
4668 4774 2.027192 TGTCATGGAGCTTAGGTGTTCC 60.027 50.000 0.00 0.00 37.76 3.62
4685 4791 3.691342 CTCCCGAGGGCGTTGTCA 61.691 66.667 2.58 0.00 35.23 3.58
4719 4825 1.141019 GGACTTGACAGCGGCGATA 59.859 57.895 12.98 0.00 0.00 2.92
4720 4826 2.125512 GGACTTGACAGCGGCGAT 60.126 61.111 12.98 0.00 0.00 4.58
4755 4862 0.318441 CTCCGTGCCTGAGTTTCTGA 59.682 55.000 0.00 0.00 0.00 3.27
4757 4864 0.605589 CTCTCCGTGCCTGAGTTTCT 59.394 55.000 0.00 0.00 0.00 2.52
4800 4907 2.725641 GTGGGCGCCGTTTTCTTT 59.274 55.556 22.54 0.00 0.00 2.52
4878 4985 3.072915 TGCCTTTCTTGAAGACCTCATGA 59.927 43.478 0.00 0.00 37.57 3.07
4895 5002 0.254178 ATCTGAACTCGCCATGCCTT 59.746 50.000 0.00 0.00 0.00 4.35
4900 5008 0.692419 AGGGGATCTGAACTCGCCAT 60.692 55.000 14.48 0.81 45.57 4.40
4909 5017 1.492176 GATTTGGAGCAGGGGATCTGA 59.508 52.381 0.00 0.00 46.18 3.27
4919 5027 2.361104 GCACCCGGATTTGGAGCA 60.361 61.111 0.73 0.00 32.33 4.26
4965 5079 0.741221 GTGTAGCAGGGAAAGGCTCG 60.741 60.000 0.00 0.00 41.41 5.03
4971 5085 2.038557 GACAAGAGGTGTAGCAGGGAAA 59.961 50.000 0.00 0.00 41.96 3.13
4973 5087 1.267121 GACAAGAGGTGTAGCAGGGA 58.733 55.000 0.00 0.00 41.96 4.20
4975 5089 0.603569 ACGACAAGAGGTGTAGCAGG 59.396 55.000 0.00 0.00 41.96 4.85
4977 5091 0.601558 GGACGACAAGAGGTGTAGCA 59.398 55.000 0.00 0.00 41.96 3.49
4999 5113 1.889573 GGCTATGCCTCTTGGTCGC 60.890 63.158 0.73 0.00 46.69 5.19
5011 5125 2.824041 GCGGTGGTGGTGGCTATG 60.824 66.667 0.00 0.00 0.00 2.23
5042 5156 4.351054 CCGCTTGGTTGGCCCTCT 62.351 66.667 0.00 0.00 0.00 3.69
5085 5199 1.415659 AGTGTCTCTCAGCTTGCAAGT 59.584 47.619 26.55 11.54 0.00 3.16
5089 5203 1.404851 GGGTAGTGTCTCTCAGCTTGC 60.405 57.143 0.00 0.00 0.00 4.01
5095 5209 3.300388 GGATCATGGGTAGTGTCTCTCA 58.700 50.000 0.00 0.00 0.00 3.27
5096 5210 2.294791 CGGATCATGGGTAGTGTCTCTC 59.705 54.545 0.00 0.00 0.00 3.20
5097 5211 2.311463 CGGATCATGGGTAGTGTCTCT 58.689 52.381 0.00 0.00 0.00 3.10
5105 5220 0.692756 TGGGAAGCGGATCATGGGTA 60.693 55.000 0.00 0.00 0.00 3.69
5111 5226 2.268920 GCACTGGGAAGCGGATCA 59.731 61.111 0.00 0.00 0.00 2.92
5112 5227 2.109126 GTGCACTGGGAAGCGGATC 61.109 63.158 10.32 0.00 0.00 3.36
5149 5264 1.003355 CTTGGTGGCTGATGTCCGT 60.003 57.895 0.00 0.00 0.00 4.69
5151 5266 1.379044 CCCTTGGTGGCTGATGTCC 60.379 63.158 0.00 0.00 0.00 4.02
5153 5268 1.380302 GACCCTTGGTGGCTGATGT 59.620 57.895 0.00 0.00 35.25 3.06
5198 5317 1.560505 GGATTGGTGGGATTGCAAGT 58.439 50.000 4.94 0.00 0.00 3.16
5200 5319 0.969917 CGGGATTGGTGGGATTGCAA 60.970 55.000 0.00 0.00 0.00 4.08
5253 5382 2.513753 CTGGTTACTCAACAATGGCCA 58.486 47.619 8.56 8.56 36.29 5.36
5260 5389 5.404946 GTCGTATAAGCTGGTTACTCAACA 58.595 41.667 0.81 0.00 36.29 3.33
5286 5415 2.024414 GTGCCTCAAACCACAGACTTT 58.976 47.619 0.00 0.00 32.37 2.66
5297 5426 0.608035 GGTTGGATCGGTGCCTCAAA 60.608 55.000 0.00 0.00 0.00 2.69
5350 5479 2.730934 ATAGCGTCAGTAGAGGTCCA 57.269 50.000 0.00 0.00 32.37 4.02
5358 5487 3.310774 GTCCTCACGTTATAGCGTCAGTA 59.689 47.826 11.98 0.00 43.83 2.74
5361 5490 1.063027 CGTCCTCACGTTATAGCGTCA 59.937 52.381 11.98 0.00 43.83 4.35
5416 5545 0.690762 GTTGGGACACCTCTGGCTAA 59.309 55.000 0.00 0.00 39.29 3.09
5427 5556 1.749665 CCTACACGTGGTTGGGACA 59.250 57.895 21.57 0.00 38.55 4.02
5440 5569 2.237143 CCAGAGTTCATTGCTCCCTACA 59.763 50.000 0.00 0.00 33.69 2.74
5442 5571 1.839994 CCCAGAGTTCATTGCTCCCTA 59.160 52.381 0.00 0.00 33.69 3.53
5453 5582 0.907230 AGTCCTCCTGCCCAGAGTTC 60.907 60.000 0.00 0.00 0.00 3.01
5459 5588 1.001760 GACCTAGTCCTCCTGCCCA 59.998 63.158 0.00 0.00 0.00 5.36
5472 5601 0.320374 CCGTGCAGGAGTTTGACCTA 59.680 55.000 8.24 0.00 45.00 3.08


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.